Difference between revisions of "Structure-based mutation analysis HEXA"
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repairPDB - done |
repairPDB - done |
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SCWRL -done |
SCWRL -done |
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| + | pdb2gmx: |
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| − | pdb2gmx: forcefield AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) (the newest) |
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watermodel: TIP3P |
watermodel: TIP3P |
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-> done very fast |
-> done very fast |
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description of the MDP file: later |
description of the MDP file: later |
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| + | Forcefiled 1: AMBER3 |
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| + | Forcefield 2: AMBER99SB-ILDN |
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| + | Forcefiled 3: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) |
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Revision as of 12:34, 30 June 2011
Farbcode bei active side: active side: grün Glycolysation: gelb Cystein: cyan Mutation:rot
Sequence Description
We had to use a PDB file, in which are no missing residues and the quality of the structure should be high. We found only one PDB structure which was not bounded to a ligand. Therefore, we could not regard the quality and the pH value, the R-factor and the coverage. Nevertheless, we listed in the following table this values:
| experiment type | X-Ray diffraction |
| Resolution | 2.8 Å |
| temperature (Kelvin) | 100K |
| temperature (Celsius) | -173 °C |
| pH-Value | 5.5 (slightly acid) |
| R-Value | 0.270 |
It was not possible to find one file, without any missing residues. In each file there was a gap between residue 74 to 89 and the last amino acid. Therefore, we decided to cut off the first 89 residues and use a PDB file with a structure from 89 - 528. This file can be found [here].
Mutations
Because of the shorten PDB file, it was not possible for us to analyse the first two mutations on position 29 and 39.
| SNP-id | codon number | mutation codon | mutation triplet |
| rs4777505 | 29 | Asn -> Ser | AAC -> AGC |
| rs121907979 | 39 | Leu -> Arg | CTT -> CGT |
| rs61731240 | 179 | His -> Asp | CAT -> GAT |
| rs121907974 | 211 | Phe -> Ser | TTC -> TCC |
| rs61747114 | 248 | Leu -> Phe | CTT -> TTT |
| rs1054374 | 293 | Ser -> Ile | AGT -> ATT |
| rs121907967 | 329 | Trp -> TER | TGG -> TAG |
| rs1800430 | 399 | Asn -> Asp | AAC -> GAC |
| rs121907982 | 436 | Ile -> Val | ATA -> GTA |
| rs121907968 | 485 | Trp -> Arg | gTGG -> CGG |
Analysis of the mutations
We created for each mutation an extra page. The summary of the analysis can be seen in the Summary Section.
Gromacs:
fetchpdb - done repairPDB - done SCWRL -done pdb2gmx:
watermodel: TIP3P
-> done very fast
description of the MDP file: later
Forcefiled 1: AMBER3
Forcefield 2: AMBER99SB-ILDN
Forcefiled 3: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
